gmane.linux.debian.devel.medical.scm
http://blog.gmane.org/gmane.linux.debian.devel.medical.scm
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1901-01-01T00:00+00:00
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-
r11014 - trunk/packages/kempbasu/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11387
<pre>Author: tille
Date: 2012-05-26 05:40:08 +0000 (Sat, 26 May 2012)
New Revision: 11014
Modified:
trunk/packages/kempbasu/trunk/debian/copyright
Log:
DEP5 skeleton
Modified: trunk/packages/kempbasu/trunk/debian/copyright
===================================================================
--- trunk/packages/kempbasu/trunk/debian/copyright2012-05-25 17:33:45 UTC (rev 11013)
+++ trunk/packages/kempbasu/trunk/debian/copyright2012-05-26 05:40:08 UTC (rev 11014)
< at >< at > -1,24 +1,10 < at >< at >
-This package was debianized by Charles Plessy <plessy< at >debian.org> on
-Tue, 27 Jan 2009 18:59:06 +0900.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://code.google.com/p/kempbasu/downloads/list
-It was downloaded from <url://example.com>
+Files: *
+Copyright: © 2007-2008 <upstream>
+License: GPL-3
-Upstream Author(s):
-
- <put author's name and email here>
- <likewise for another author>
-
-Copyright:
-
- <Copyright (C) YYYY Name OfAuthor>
- <likewise for another author>
-
-License: GPL-3+
-
- <Put the license of the package here indented by 4 spaces>
-
-The Debian packaging is copyright 2009, Charles Plessy <plessy< at >debian.org> and
-is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
+Files: debian/*
+Copyright: © 2009 Charles Plessy <plessy< at >debian.org>
+License: GPL-3
_______________________________________________
debian-med-commit mailing list
debian-med-commit< at >lists.alioth.debian.org
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Andreas Tille
2012-05-26T05:40:09
-
r11013 - trunk/packages/haploview/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11386
<pre>Author: tille
Date: 2012-05-25 17:33:45 +0000 (Fri, 25 May 2012)
New Revision: 11013
Modified:
trunk/packages/haploview/trunk/debian/changelog
trunk/packages/haploview/trunk/debian/control
trunk/packages/haploview/trunk/debian/copyright
Log:
Fixing machine readable information
Modified: trunk/packages/haploview/trunk/debian/changelog
===================================================================
--- trunk/packages/haploview/trunk/debian/changelog2012-05-25 17:27:06 UTC (rev 11012)
+++ trunk/packages/haploview/trunk/debian/changelog2012-05-25 17:33:45 UTC (rev 11013)
< at >< at > -1,4 +1,4 < at >< at >
-haploview (4.0-1) UNRELEASED; urgency=low
+haploview (4.1-1) UNRELEASED; urgency=low
* Initial release (Closes: #311421)
Modified: trunk/packages/haploview/trunk/debian/control
===================================================================
--- trunk/packages/haploview/trunk/debian/control2012-05-25 17:27:06 UTC (rev 11012)
+++ trunk/packages/haploview/trunk/debian/control2012-05-25 17:33:45 UTC (rev 11013)
< at >< at > -1,10 +1,14 < at >< at >
Source: haploview
Section: contrib/science
-Priority: extra
-Maintainer: Steffen Moeller <steffen_moeller< at >gmx.de>
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <steffen_moeller< at >gmx.de>
Build-Depends-Indep: cdbs, ant, debhelper (>= 5), kaffe|java-compiler, libjfreechart-java, libjgrapht-java, liblog4j1.2-java, javahelp2, quilt
Standards-Version: 3.7.3
Homepage: http://www.broad.mit.edu/mpg/haploview/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/haploview/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/haploview/trunk/
Package: haploview
Architecture: all
Modified: trunk/packages/haploview/trunk/debian/copyright
===================================================================
--- trunk/packages/haploview/trunk/debian/copyright2012-05-25 17:27:06 UTC (rev 11012)
+++ trunk/packages/haploview/trunk/debian/copyright2012-05-25 17:33:45 UTC (rev 11013)
< at >< at > -1,19 +1,32 < at >< at >
-This package was debianized by Steffen Moeller <steffen_moeller< at >gmx.de> on
-Sun, 14 Jan 2007 15:28:10 +0100.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: HaploView
+Upstream-Contact: Jeffrey Barrett, Julian Maller, David Bender <haploview< at >broad.mit.edu>
+Source: http://sourceforge.net/projects/haploview/files/haploview-source/
-It was downloaded from www.sf.net/projects/haploview.
+Files: *
+Copyright: © 2003-2006 Broad Institute of MIT and Harvard
+License: MIT
-Upstream Authors: Jeffrey Barrett, Julian Maller, David Bender <haploview< at >broad.mit.edu>
+Files: debian/*
+Copyright: © 2007 Steffen Moeller <steffen_moeller< at >gmx.de>
+License: MIT
-Copyright: 2003-2006 Broad Institute of MIT and Harvard
-
-License:
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-
-The Debian packaging is (C) 2007, Steffen Moeller <steffen_moeller< at >gmx.de> and
-is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restr iction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Soft ware is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING F ROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
_______________________________________________
debian-med-commit mailing list
debian-med-commit< at >lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit</pre>
Andreas Tille
2012-05-25T17:33:45
-
r11012 - in trunk: . package_template
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11385
<pre>Author: tille
Date: 2012-05-25 17:27:06 +0000 (Fri, 25 May 2012)
New Revision: 11012
Added:
trunk/package_template/
trunk/package_template/changelog
trunk/package_template/compat
trunk/package_template/control
trunk/package_template/copyright
trunk/package_template/rules
trunk/package_template/upstream
Log:
Very simple template for machine-readable files to simplify creating new packages which are typical for Debian Med team
Added: trunk/package_template/changelog
===================================================================
--- trunk/package_template/changelog (rev 0)
+++ trunk/package_template/changelog2012-05-25 17:27:06 UTC (rev 11012)
< at >< at > -0,0 +1,5 < at >< at >
+<pkg> (<version>-1) unstable; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- DMPT <debian-med-packaging< at >lists.alioth.debian.org> <date>
Added: trunk/package_template/compat
===================================================================
--- trunk/package_template/compat (rev 0)
+++ trunk/package_template/compat2012-05-25 17:27:06 UTC (rev 11012)
< at >< at > -0,0 +1 < at >< at >
+9
Added: trunk/package_template/control
===================================================================
--- trunk/package_template/control (rev 0)
+++ trunk/package_template/control2012-05-25 17:27:06 UTC (rev 11012)
< at >< at > -0,0 +1,17 < at >< at >
+Source: <pkg>
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille< at >debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.3
+Homepage: <homepage>
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/<pkg>/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/<pkg>/trunk/
+
+Package: <pkg>
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: <short_description>
+ <long_description>
Added: trunk/package_template/copyright
===================================================================
--- trunk/package_template/copyright (rev 0)
+++ trunk/package_template/copyright2012-05-25 17:27:06 UTC (rev 11012)
< at >< at > -0,0 +1,11 < at >< at >
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Source: <path_to_download>
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille< at >debian.org>
+License: <license>
Added: trunk/package_template/rules
===================================================================
--- trunk/package_template/rules (rev 0)
+++ trunk/package_template/rules2012-05-25 17:27:06 UTC (rev 11012)
< at >< at > -0,0 +1,6 < at >< at >
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+dh $< at >
Property changes on: trunk/package_template/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/package_template/upstream
===================================================================
--- trunk/package_template/upstream (rev 0)
+++ trunk/package_template/upstream2012-05-25 17:27:06 UTC (rev 11012)
< at >< at > -0,0 +1,12 < at >< at >
+Reference:
+ Author:
+ Title:
+ Journal:
+ Year:
+ Volume:
+ Number:
+ Pages:
+ DOI:
+ PMID:
+ URL:
+ eprint:
_______________________________________________
debian-med-commit mailing list
debian-med-commit< at >lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit</pre>
Andreas Tille
2012-05-25T17:27:07
-
r11011 - trunk/packages/haploview
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11384
<pre>Author: tille
Date: 2012-05-25 17:19:46 +0000 (Fri, 25 May 2012)
New Revision: 11011
Removed:
trunk/packages/haploview/branches/
Log:
There is no point in keeping upstream stuff in SVN
</pre>
Andreas Tille
2012-05-25T17:19:46
-
r11010 - trunk/packages/grogui/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11383
<pre>Author: tille
Date: 2012-05-25 13:19:36 +0000 (Fri, 25 May 2012)
New Revision: 11010
Modified:
trunk/packages/grogui/trunk/debian/control
Log:
Take over better description from task file
Modified: trunk/packages/grogui/trunk/debian/control
===================================================================
--- trunk/packages/grogui/trunk/debian/control2012-05-25 13:17:41 UTC (rev 11009)
+++ trunk/packages/grogui/trunk/debian/control2012-05-25 13:19:36 UTC (rev 11010)
< at >< at > -9,6 +9,15 < at >< at >
Package: grogui
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: <insert up to 60 chars description>
+Description: graphical user interface for popular molecular dynamics package GROMACS
Gromacs GUI is a Qt4-based graphical user interface for widely used molecular
dynamics package, GROMACS.
+ .
+ 1. File browsing and management with customizable right-click pop up menu.
+ 2. Graphical interfaces for GROMACS commands (currently 21 commands have their own interfaces).
+ 3. Plot drawing tool which can export plots to pdf.
+ 4. A simple built-in console.
+ 5. Built-in GROMACS manual viewer.
+ 6. Built-in file editor with syntax highlighting for some GROMACS file formats (currently only mdp format is supported).
+ 7. MDP Writer section to easily create your mdp files.
+ 8. File icons based on their types.
</pre>
Andreas Tille
2012-05-25T13:19:37
-
r11009 - trunk/packages/grogui/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11382
<pre>Author: tille
Date: 2012-05-25 13:17:41 +0000 (Fri, 25 May 2012)
New Revision: 11009
Modified:
trunk/packages/grogui/trunk/debian/copyright
Log:
DEP5
Modified: trunk/packages/grogui/trunk/debian/copyright
===================================================================
--- trunk/packages/grogui/trunk/debian/copyright2012-05-25 12:49:42 UTC (rev 11008)
+++ trunk/packages/grogui/trunk/debian/copyright2012-05-25 13:17:41 UTC (rev 11009)
< at >< at > -1,40 +1,30 < at >< at >
-This package was debianized by:
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Gromacs GUI
+Source: http://kde-apps.org/content/show.php/Gromacs+GUI+?content=47665
- Steffen Moeller <moeller< at >debian.org> on Sun, 23 Nov 2008 23:38:26 +0100
+Files: *
+Copyright: © 2008 Reza Salari <resal81< at >yahoo.com>
+License: GPL-2+
-It was downloaded from:
+Files: debian/*
+Copyright: © 2008 Steffen Moeller <moeller< at >debian.org>
+License: GPL-2+
- http://resal.wordpress.com/gromacs-gui/
-
-Upstream Author:
-
- Reza Salari <resal81< at >yahoo.com>
-
-Copyright:
-
- Copyright (C) 2008 Reza Salari <resal81< at >yahoo.com>
-
-License:
-
+License: GPL-2+
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
-
+ .
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
-
+ .
You should have received a copy of the GNU General Public License
along with this package; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL'.
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
-The Debian packaging is:
-
- Copyright C) 2008, Steffen Moeller <moeller< at >debian.org>
-
-and is licensed under the GPL, see above.
_______________________________________________
debian-med-commit mailing list
debian-med-commit< at >lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit</pre>
Andreas Tille
2012-05-25T13:17:42
-
r11008 - in trunk/packages/libhmsbeagle/trunk/debian: .patches
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11381
<pre>Author: tille
Date: 2012-05-25 12:49:42 +0000 (Fri, 25 May 2012)
New Revision: 11008
Removed:
trunk/packages/libhmsbeagle/trunk/debian/patches/do_not_build_unused_plugin.patch
Modified:
trunk/packages/libhmsbeagle/trunk/debian/changelog
trunk/packages/libhmsbeagle/trunk/debian/patches/enable_static.patch
trunk/packages/libhmsbeagle/trunk/debian/patches/series
Log:
Restore preparation for new upstream version - waiting for answer from upstream
Modified: trunk/packages/libhmsbeagle/trunk/debian/changelog
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/changelog2012-05-25 12:48:02 UTC (rev 11007)
+++ trunk/packages/libhmsbeagle/trunk/debian/changelog2012-05-25 12:49:42 UTC (rev 11008)
< at >< at > -1,3 +1,12 < at >< at >
+libhmsbeagle (1.1-1) UNRELEASED; urgency=low
+
+ * New upstream release
+ - debian/patches/disable_cpu_sse_plugin.patch: Seems upstream
+ has solved the problem a bit differently than in this patch
+ -> droping it for the moment
+
+ -- Andreas Tille <tille< at >debian.org> Fri, 25 May 2012 14:48:52 +0200
+
libhmsbeagle (1.0-6) unstable; urgency=low
* debian/upstream:
Deleted: trunk/packages/libhmsbeagle/trunk/debian/patches/do_not_build_unused_plugin.patch
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/patches/do_not_build_unused_plugin.patch2012-05-25 12:48:02 UTC (rev 11007)
+++ trunk/packages/libhmsbeagle/trunk/debian/patches/do_not_build_unused_plugin.patch2012-05-25 12:49:42 UTC (rev 11008)
< at >< at > -1,31 +0,0 < at >< at >
-Author: Andreas Tille <tille< at >debian.org>
-Bug-Closed: http://bugs.debian.org/656755
-Date: Sat, 21 Jan 2012 17:27:53 +0100
-Description: According to the bug reporter the plugin causes
- trouble on all architectures but amd64. Because this plugin
- is finally not used at all the building will be simply
- suppressed
-
-That's too simple and does not work - it results in
-
-../../libhmsbeagle/.libs/libhmsbeagle.so: undefined reference to `beagle::plugin::PluginManager::instance()'
-../../libhmsbeagle/.libs/libhmsbeagle.so: undefined reference to `beagle::plugin::PluginManager::findPlugin(char const*)'
-
-
---- libhmsbeagle-1.0.orig/libhmsbeagle/Makefile.am
-+++ libhmsbeagle-1.0/libhmsbeagle/Makefile.am
-< at >< at > -1,4 +1,4 < at >< at >
--SUBDIRS=GPU CPU plugin
-+SUBDIRS=GPU CPU
- if BUILDJNI
- lib_LTLIBRARIES=libhmsbeagle.la libhmsbeagle-jni.la
- else
-< at >< at > -6,7 +6,7 < at >< at >
- endif
-
- libhmsbeagle_la_SOURCES=beagle.cpp BeagleImpl.h
--libhmsbeagle_la_LIBADD = plugin/libplugin.la
-+# libhmsbeagle_la_LIBADD = plugin/libplugin.la
- libhmsbeagle_la_CXXFLAGS = $(AM_CXXFLAGS)
- libhmsbeagle_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION)
-
Modified: trunk/packages/libhmsbeagle/trunk/debian/patches/enable_static.patch
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/patches/enable_static.patch2012-05-25 12:48:02 UTC (rev 11007)
+++ trunk/packages/libhmsbeagle/trunk/debian/patches/enable_static.patch2012-05-25 12:49:42 UTC (rev 11008)
< at >< at > -2,8 +2,8 < at >< at >
Date: Sat, 21 Jan 2012 17:27:53 +0100
Description: Enable building static libraries for the -dev package
---- libhmsbeagle-1.0.orig/configure.ac
-+++ libhmsbeagle-1.0/configure.ac
+--- libhmsbeagle-1.1.orig/configure.ac
++++ libhmsbeagle-1.1/configure.ac
< at >< at > -59,8 +59,8 < at >< at >
AC_PROG_CXX
AC_PROG_INSTALL
Modified: trunk/packages/libhmsbeagle/trunk/debian/patches/series
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/patches/series2012-05-25 12:48:02 UTC (rev 11007)
+++ trunk/packages/libhmsbeagle/trunk/debian/patches/series2012-05-25 12:49:42 UTC (rev 11008)
< at >< at > -1,3 +1 < at >< at >
enable_static.patch
-disable_cpu_sse_plugin.patch
-gcc-4.7.patch
</pre>
Andreas Tille
2012-05-25T12:49:43
-
r11007 - in trunk/packages/libhmsbeagle/trunk/debian: .patches
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11380
<pre>Author: tille
Date: 2012-05-25 12:48:02 +0000 (Fri, 25 May 2012)
New Revision: 11007
Added:
trunk/packages/libhmsbeagle/trunk/debian/patches/do_not_build_unused_plugin.patch
Modified:
trunk/packages/libhmsbeagle/trunk/debian/changelog
trunk/packages/libhmsbeagle/trunk/debian/patches/enable_static.patch
trunk/packages/libhmsbeagle/trunk/debian/patches/series
Log:
Override unconfirmed NMU with current changes in SVN; upgrade to new version needs more communication with upstream and is thus delayed; also delayed hardening
Modified: trunk/packages/libhmsbeagle/trunk/debian/changelog
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/changelog2012-05-25 12:29:48 UTC (rev 11006)
+++ trunk/packages/libhmsbeagle/trunk/debian/changelog2012-05-25 12:48:02 UTC (rev 11007)
< at >< at > -1,9 +1,5 < at >< at >
-libhmsbeagle (1.1-1) UNRELEASED; urgency=low
+libhmsbeagle (1.0-6) unstable; urgency=low
- * New upstream release
- - debian/patches/disable_cpu_sse_plugin.patch: Seems upstream
- has solved the problem a bit differently than in this patch
- -> droping it for the moment
* debian/upstream:
- Make authors BibTeX compliant
- Add some publication info (volume, number, pages)
Added: trunk/packages/libhmsbeagle/trunk/debian/patches/do_not_build_unused_plugin.patch
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/patches/do_not_build_unused_plugin.patch (rev 0)
+++ trunk/packages/libhmsbeagle/trunk/debian/patches/do_not_build_unused_plugin.patch2012-05-25 12:48:02 UTC (rev 11007)
< at >< at > -0,0 +1,31 < at >< at >
+Author: Andreas Tille <tille< at >debian.org>
+Bug-Closed: http://bugs.debian.org/656755
+Date: Sat, 21 Jan 2012 17:27:53 +0100
+Description: According to the bug reporter the plugin causes
+ trouble on all architectures but amd64. Because this plugin
+ is finally not used at all the building will be simply
+ suppressed
+
+That's too simple and does not work - it results in
+
+../../libhmsbeagle/.libs/libhmsbeagle.so: undefined reference to `beagle::plugin::PluginManager::instance()'
+../../libhmsbeagle/.libs/libhmsbeagle.so: undefined reference to `beagle::plugin::PluginManager::findPlugin(char const*)'
+
+
+--- libhmsbeagle-1.0.orig/libhmsbeagle/Makefile.am
++++ libhmsbeagle-1.0/libhmsbeagle/Makefile.am
+< at >< at > -1,4 +1,4 < at >< at >
+-SUBDIRS=GPU CPU plugin
++SUBDIRS=GPU CPU
+ if BUILDJNI
+ lib_LTLIBRARIES=libhmsbeagle.la libhmsbeagle-jni.la
+ else
+< at >< at > -6,7 +6,7 < at >< at >
+ endif
+
+ libhmsbeagle_la_SOURCES=beagle.cpp BeagleImpl.h
+-libhmsbeagle_la_LIBADD = plugin/libplugin.la
++# libhmsbeagle_la_LIBADD = plugin/libplugin.la
+ libhmsbeagle_la_CXXFLAGS = $(AM_CXXFLAGS)
+ libhmsbeagle_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION)
+
Modified: trunk/packages/libhmsbeagle/trunk/debian/patches/enable_static.patch
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/patches/enable_static.patch2012-05-25 12:29:48 UTC (rev 11006)
+++ trunk/packages/libhmsbeagle/trunk/debian/patches/enable_static.patch2012-05-25 12:48:02 UTC (rev 11007)
< at >< at > -2,8 +2,8 < at >< at >
Date: Sat, 21 Jan 2012 17:27:53 +0100
Description: Enable building static libraries for the -dev package
---- libhmsbeagle-1.1.orig/configure.ac
-+++ libhmsbeagle-1.1/configure.ac
+--- libhmsbeagle-1.0.orig/configure.ac
++++ libhmsbeagle-1.0/configure.ac
< at >< at > -59,8 +59,8 < at >< at >
AC_PROG_CXX
AC_PROG_INSTALL
Modified: trunk/packages/libhmsbeagle/trunk/debian/patches/series
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/patches/series2012-05-25 12:29:48 UTC (rev 11006)
+++ trunk/packages/libhmsbeagle/trunk/debian/patches/series2012-05-25 12:48:02 UTC (rev 11007)
< at >< at > -1 +1,3 < at >< at >
enable_static.patch
+disable_cpu_sse_plugin.patch
+gcc-4.7.patch
</pre>
Andreas Tille
2012-05-25T12:48:02
-
r11006 - trunk/packages/libforester-java/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11379
<pre>Author: osallou
Date: 2012-05-25 12:29:48 +0000 (Fri, 25 May 2012)
New Revision: 11006
Modified:
trunk/packages/libforester-java/trunk/debian/control
Log:
fix dependency name
Modified: trunk/packages/libforester-java/trunk/debian/control
===================================================================
--- trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:26:45 UTC (rev 11005)
+++ trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:29:48 UTC (rev 11006)
< at >< at > -23,7 +23,7 < at >< at >
Package: libforester-java
Architecture: all
Depends: ${misc:Depends},
- libcommons-codec, libitext-java
+ libcommons-codec-java, libitext-java
Description: Libraries for evolutionary biology and comparative genomics research
Forester is a library of Java software for phylogenomics
and evolutionary biology research. It can be used to read or
</pre>
Olivier Sallou
2012-05-25T12:29:49
-
r11005 - trunk/packages/libforester-java/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11378
<pre>Author: osallou
Date: 2012-05-25 12:26:45 +0000 (Fri, 25 May 2012)
New Revision: 11005
Modified:
trunk/packages/libforester-java/trunk/debian/control
Log:
fix dependency name
Modified: trunk/packages/libforester-java/trunk/debian/control
===================================================================
--- trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:12:50 UTC (rev 11004)
+++ trunk/packages/libforester-java/trunk/debian/control2012-05-25 12:26:45 UTC (rev 11005)
< at >< at > -5,7 +5,7 < at >< at >
DM-Upload-Allowed: yes
Uploaders: Olivier Sallou <osallou< at >debian.org>
Build-Depends: debhelper (>= 8.0.0),
- default-jdk, junit4, javahelper (>=0.25), libcommons-codec, libitext-java
+ default-jdk, junit4, javahelper (>=0.25), libcommons-codec-java, libitext-java
Standards-Version: 3.9.3
Homepage: http://code.google.com/p/forester
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/forester/trunk/
</pre>
Olivier Sallou
2012-05-25T12:26:46
-
r11004 - trunk/packages/fasttree/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11377
<pre>Author: tille
Date: 2012-05-25 12:12:50 +0000 (Fri, 25 May 2012)
New Revision: 11004
Modified:
trunk/packages/fasttree/trunk/debian/copyright
Log:
DEP5
Modified: trunk/packages/fasttree/trunk/debian/copyright
===================================================================
--- trunk/packages/fasttree/trunk/debian/copyright2012-05-25 12:07:10 UTC (rev 11003)
+++ trunk/packages/fasttree/trunk/debian/copyright2012-05-25 12:12:50 UTC (rev 11004)
< at >< at > -1,10 +1,8 < at >< at >
-Format: http://dep.debian.net/deps/dep5
-Upstream-Name: fasttree
-Source: <url://example.com>
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: FastTree
+Source: http://www.microbesonline.org/fasttree/#Install
Files: *
-Copyright: <years> <put author's name and email here>
- <years> <likewise for another author>
Copyright: (C) 2008-2009 The Regents of the University of California
License: GPL-2.0+
< at >< at > -29,13 +27,3 < at >< at >
On Debian systems, the complete text of the GNU General
Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
-# Please choose a license for your packaging work. If the program you package
-# uses a mainstream license, using the same license is the safest choice.
-# Please avoid to pick license terms that are more restrictive than the
-# packaged work, as it may make Debian's contributions unacceptable upstream.
-# If you just want it to be GPL version 3, leave the following line in.
-
-and is licensed under the GPL version 3, see above.
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
</pre>
Andreas Tille
2012-05-25T12:12:50
-
r11003 - trunk/packages/ecell/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11376
<pre>Author: tille
Date: 2012-05-25 12:07:10 +0000 (Fri, 25 May 2012)
New Revision: 11003
Modified:
trunk/packages/ecell/trunk/debian/copyright
Log:
Pseudo-DEP5 to enable machine-readable gatherer fetch license
Modified: trunk/packages/ecell/trunk/debian/copyright
===================================================================
--- trunk/packages/ecell/trunk/debian/copyright2012-05-25 12:02:58 UTC (rev 11002)
+++ trunk/packages/ecell/trunk/debian/copyright2012-05-25 12:07:10 UTC (rev 11003)
< at >< at > -1,10 +1,11 < at >< at >
-This package was debianized by Steffen Moeller <moeller< at >unknown> on
-Wed, 10 Mar 2004 22:08:00 +0100.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: E-Cell
+Source: https://github.com/ecell/ecell.github.com
-It was downloaded from <fill in ftp site>
+Files: *
+Copyright: © -2003 ???
+License: GPL
-Upstream Author(s): <put author(s) name and email here>
-
-Copyright:
-
-<Must follow here>
+Files: debian/*
+Copyright: © 2004 Steffen Moeller <moeller< at >debian.org>
+License: GPL
_______________________________________________
debian-med-commit mailing list
debian-med-commit< at >lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit</pre>
Andreas Tille
2012-05-25T12:07:11
-
r11002 - trunk/packages/ecell/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11375
<pre>Author: tille
Date: 2012-05-25 12:02:58 +0000 (Fri, 25 May 2012)
New Revision: 11002
Modified:
trunk/packages/ecell/trunk/debian/control
Log:
Team maintained package
Modified: trunk/packages/ecell/trunk/debian/control
===================================================================
--- trunk/packages/ecell/trunk/debian/control2012-05-25 11:48:20 UTC (rev 11001)
+++ trunk/packages/ecell/trunk/debian/control2012-05-25 12:02:58 UTC (rev 11002)
< at >< at > -1,7 +1,9 < at >< at >
Source: ecell
Section: science
Priority: optional
-Maintainer: Steffen Moeller <moeller< at >pzr.uni-rostock.de>
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller< at >pzr.uni-rostock.de>
Build-Depends: debhelper (>= 4.0.0), python-numpy, python-dev, python-gtk2, python-glade2, g++ (>= 3.3), libgsl0-dev, libboost-python-dev, automake, autoconf, libtool, python-gnome2, expect, doxygen, graphviz, docbook-utils, ghostscript, docbook-to-man
Standards-Version: 3.6.0
Homepage: http://www.e-cell.org/
</pre>
Andreas Tille
2012-05-25T12:02:58
-
r11001 - in trunk/packages: . logomat-m logomat-m/trunklogomat-m/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11374
<pre>Author: tille
Date: 2012-05-25 11:48:20 +0000 (Fri, 25 May 2012)
New Revision: 11001
Added:
trunk/packages/logomat-m/
trunk/packages/logomat-m/trunk/
trunk/packages/logomat-m/trunk/debian/
trunk/packages/logomat-m/trunk/debian/changelog
trunk/packages/logomat-m/trunk/debian/compat
trunk/packages/logomat-m/trunk/debian/control
trunk/packages/logomat-m/trunk/debian/copyright
trunk/packages/logomat-m/trunk/debian/upstream
Log:
Inject data from med-bio task file as machine readable packaging files to enable machine-readable gatherer fetching it
Added: trunk/packages/logomat-m/trunk/debian/changelog
===================================================================
--- trunk/packages/logomat-m/trunk/debian/changelog (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/changelog2012-05-25 11:48:20 UTC (rev 11001)
< at >< at > -0,0 +1,5 < at >< at >
+logomat-m (0.0.20091119-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Andreas Tille <tille< at >debian.org> Thu, 24 May 2012 14:30:13 +0200
Added: trunk/packages/logomat-m/trunk/debian/compat
===================================================================
--- trunk/packages/logomat-m/trunk/debian/compat (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/compat2012-05-25 11:48:20 UTC (rev 11001)
< at >< at > -0,0 +1 < at >< at >
+9
Added: trunk/packages/logomat-m/trunk/debian/control
===================================================================
--- trunk/packages/logomat-m/trunk/debian/control (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/control2012-05-25 11:48:20 UTC (rev 11001)
< at >< at > -0,0 +1,27 < at >< at >
+Source: logomat-m
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille< at >debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.3
+Homepage: http://www.sanger.ac.uk/resources/software/logomat-m/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/logomat-m/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/logomat-m/trunk/
+
+Package: logomat-m
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: visualize central aspects of Profile Hidden Markov Models (pHMMs)
+ Profile Hidden Markov Models (pHMMs) are a widely used tool for
+ protein family research. We present a method to visualize all of
+ their central aspects graphically, thus generalizing the concept of
+ sequence logos introduced by Schneider and Stephens. For each
+ emitting state of the pHMM, we display a stack of letters. As for
+ sequence logos, the stack height is determined by the deviation of
+ the position's letter emission frequencies from the background
+ frequencies of the letters. As a new feature, the stack width now
+ visualizes both the probability of reaching the state (the hitting
+ probability) and the expected number of letters the state emits
+ during a pass through the model (the expected contribution).
Added: trunk/packages/logomat-m/trunk/debian/copyright
===================================================================
--- trunk/packages/logomat-m/trunk/debian/copyright (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/copyright2012-05-25 11:48:20 UTC (rev 11001)
< at >< at > -0,0 +1,11 < at >< at >
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: LogoMat-M
+Source: ftp://ftp.sanger.ac.uk/pub4/resources/software/logomat-m/
+
+Files: *
+Copyright: © -2009 ???
+License: Artistic
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille< at >debian.org>
+License: Artistic
Added: trunk/packages/logomat-m/trunk/debian/upstream
===================================================================
--- trunk/packages/logomat-m/trunk/debian/upstream (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/upstream2012-05-25 11:48:20 UTC (rev 11001)
< at >< at > -0,0 +1,11 < at >< at >
+Reference:
+ Author: Benjamin Schuster-Böckler and Jörg Schultz and Sven Rahmann
+ Title: HMM Logos for visualization of protein families
+ Journal: BMC Bioinformatics
+ Year: 2004
+ Volume: 5
+ Pages: 7
+ DOI: 10.1186/1471-2105-5-7
+ PMID: 14736340
+ URL: http://www.biomedcentral.com/1471-2105/5/7
+ eprint: http://www.biomedcentral.com/content/pdf/1471-2105-5-7.pdf
_______________________________________________
debian-med-commit mailing list
debian-med-commit< at >lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit</pre>
Andreas Tille
2012-05-25T11:48:20
-
r11000 - in trunk/packages/dcmtk/trunk/debian: . patches
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11373
<pre>Author: malat
Date: 2012-05-25 09:51:25 +0000 (Fri, 25 May 2012)
New Revision: 11000
Added:
trunk/packages/dcmtk/trunk/debian/patches/bug674361.patch
Modified:
trunk/packages/dcmtk/trunk/debian/changelog
trunk/packages/dcmtk/trunk/debian/control
trunk/packages/dcmtk/trunk/debian/patches/series
trunk/packages/dcmtk/trunk/debian/rules
Log:
Work on dcmtk package/gcc 4.7 issue
Modified: trunk/packages/dcmtk/trunk/debian/changelog
===================================================================
--- trunk/packages/dcmtk/trunk/debian/changelog2012-05-25 08:46:12 UTC (rev 10999)
+++ trunk/packages/dcmtk/trunk/debian/changelog2012-05-25 09:51:25 UTC (rev 11000)
< at >< at > -1,3 +1,11 < at >< at >
+dcmtk (3.6.0-11) UNRELEASED; urgency=low
+
+ * Fix compilation with gcc 4.7. Closes: #674361
+ - debian/patches/bug674361.patch
+ * Make sure to link against libxml2
+
+ -- Mathieu Malaterre <malat< at >debian.org> Fri, 25 May 2012 11:19:22 +0200
+
dcmtk (3.6.0-10) unstable; urgency=low
[ Andreas Tille ]
Modified: trunk/packages/dcmtk/trunk/debian/control
===================================================================
--- trunk/packages/dcmtk/trunk/debian/control2012-05-25 08:46:12 UTC (rev 10999)
+++ trunk/packages/dcmtk/trunk/debian/control2012-05-25 09:51:25 UTC (rev 11000)
< at >< at > -5,8 +5,8 < at >< at >
DM-Upload-Allowed: yes
Uploaders: Juergen Salk <jsa< at >debian.org>,
Andreas Tille <tille< at >debian.org>,
- Mathieu Malaterre <mathieu.malaterre< at >gmail.com>
-Build-Depends: debhelper (>= 7), autoconf, autotools-dev, zlib1g-dev, libtiff-dev, quilt,
+ Mathieu Malaterre <malat< at >debian.org>
+Build-Depends: debhelper (>= 9), autoconf, autotools-dev, zlib1g-dev, libtiff-dev, quilt,
libpng-dev, libxml2-dev, libwrap0-dev, libssl-dev, doxygen (>= 1.7.4), graphviz, libcharls-dev
Standards-Version: 3.9.3
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/dcmtk/trunk/
Added: trunk/packages/dcmtk/trunk/debian/patches/bug674361.patch
===================================================================
--- trunk/packages/dcmtk/trunk/debian/patches/bug674361.patch (rev 0)
+++ trunk/packages/dcmtk/trunk/debian/patches/bug674361.patch2012-05-25 09:51:25 UTC (rev 11000)
< at >< at > -0,0 +1,1015 < at >< at >
+From dbadc0d8f3760f65504406c8b2cb8633f868a258 Mon Sep 17 00:00:00 2001
+From: Joerg Riesmeier <dicom< at >offis.de>
+Date: Thu, 17 Nov 2011 16:13:14 +0000
+Subject: [PATCH] Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
+
+---
+ CHANGES.361 | 24 ++++++++++++++++++++++++
+ dcmimage/include/dcmtk/dcmimage/diargpxt.h | 25 ++++++++++++++-----------
+ dcmimage/include/dcmtk/dcmimage/dicmypxt.h | 11 +++++++----
+ dcmimage/include/dcmtk/dcmimage/dicocpt.h | 11 +++++++----
+ dcmimage/include/dcmtk/dcmimage/dicoflt.h | 17 ++++++++++-------
+ dcmimage/include/dcmtk/dcmimage/dicorot.h | 17 ++++++++++-------
+ dcmimage/include/dcmtk/dcmimage/dicosct.h | 13 ++++++++-----
+ dcmimage/include/dcmtk/dcmimage/dihsvpxt.h | 11 +++++++----
+ dcmimage/include/dcmtk/dcmimage/dipalpxt.h | 11 +++++++----
+ dcmimage/include/dcmtk/dcmimage/dirgbpxt.h | 15 +++++++++------
+ dcmimage/include/dcmtk/dcmimage/diybrpxt.h | 15 +++++++++------
+ dcmimage/include/dcmtk/dcmimage/diyf2pxt.h | 11 +++++++----
+ dcmimage/include/dcmtk/dcmimage/diyp2pxt.h | 11 +++++++----
+ dcmimgle/include/dcmtk/dcmimgle/diflipt.h | 11 +++++++----
+ dcmimgle/include/dcmtk/dcmimgle/dimoflt.h | 15 +++++++++------
+ dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h | 13 ++++++++-----
+ dcmimgle/include/dcmtk/dcmimgle/dimorot.h | 15 +++++++++------
+ dcmimgle/include/dcmtk/dcmimgle/dimosct.h | 11 +++++++----
+ dcmimgle/include/dcmtk/dcmimgle/dirotat.h | 11 +++++++----
+ dcmimgle/include/dcmtk/dcmimgle/discalet.h | 19 +++++++++++--------
+ ofstd/include/dcmtk/ofstd/ofoset.h | 13 ++++++++-----
+ ofstd/libsrc/ofchrenc.cc | 13 +++++++++++--
+ 22 files changed, 203 insertions(+), 110 deletions(-)
+
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diargpxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diargpxt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diargpxt.h2012-05-25 09:16:23.791876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomARGBPixelTemplate (Header) - UNTESTED !!!
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:29 $
+- * CVS/RCS Revision: $Revision: 1.21 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.22 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -91,7 +91,7 < at >< at >
+ const unsigned long planeSize,
+ const int bits)
+ { // not very much optimized, but no one really uses ARGB !!
+- if (Init(pixel))
++ if (this->Init(pixel))
+ {
+ register T2 value;
+ const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1));
+< at >< at > -103,9 +103,9 < at >< at >
+ /*
+ register const T1 *a = pixel; // points to alpha plane
+ const T1 *rgb[3];
+- rgb[0] = a + this->InputCount; // points to red plane
+- rgb[1] = rgb[0] + this->InputCount; // points to green plane
+- rgb[2] = rgb[1] + this->InputCount; // points to blue plane
++ rgb[0] = a + this->InputCount; // points to red plane
++ rgb[1] = rgb[0] + this->InputCount; // points to green plane
++ rgb[2] = rgb[1] + this->InputCount; // points to blue plane
+ for (i = 0; i < count; ++i)
+ {
+ value = OFstatic_cast(T2, *(a++)); // get alpha value
+< at >< at > -141,10 +141,10 < at >< at >
+ /* convert a single frame */
+ for (l = planeSize; (l != 0) && (i < count); --l, ++i)
+ {
+- value = OFstatic_cast(T2, *(a++)); // get alpha value
++ value = OFstatic_cast(T2, *(a++)); // get alpha value
+ if (value > 0)
+ {
+- for (int j = 0; j < 3; ++j) // set palette color
++ for (int j = 0; j < 3; ++j) // set palette color
+ {
+ if (value <= palette[j]->getFirstEntry(value))
+ this->Data[j][i] = OFstatic_cast(T3, palette[j]->getFirstValue());
+< at >< at > -152,12 +152,12 < at >< at >
+ this->Data[j][i] = OFstatic_cast(T3, palette[j]->getLastValue());
+ else
+ this->Data[j][i] = OFstatic_cast(T3, palette[j]->getValue(value));
+- ++rgb[j]; // skip RGB values
++ ++rgb[j]; // skip RGB values
+ }
+ }
+ else
+ {
+- for (int j = 0; j < 3; ++j) // copy RGB values
++ for (int j = 0; j < 3; ++j) // copy RGB values
+ this->Data[j][i] = OFstatic_cast(T3, removeSign(*(rgb[j]++), offset));
+ }
+ }
+< at >< at > -204,6 +204,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: diargpxt.h,v $
++ * Revision 1.22 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.21 2010-10-14 13:16:29 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicmypxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicmypxt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicmypxt.h2012-05-25 09:16:23.791876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomCMYKPixelTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:29 $
+- * CVS/RCS Revision: $Revision: 1.20 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.21 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -87,7 +87,7 < at >< at >
+ const unsigned long planeSize,
+ const int bits)
+ {
+- if (Init(pixel))
++ if (this->Init(pixel))
+ {
+ // use the number of input pixels derived from the length of the 'PixelData'
+ // attribute), but not more than the size of the intermediate buffer
+< at >< at > -157,6 +157,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dicmypxt.h,v $
++ * Revision 1.21 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.20 2010-10-14 13:16:29 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicocpt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicocpt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicocpt.h2012-05-25 09:16:23.791876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1998-2010, OFFIS e.V.
++ * Copyright (C) 1998-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomColorCopyTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:29 $
+- * CVS/RCS Revision: $Revision: 1.12 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.13 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -86,7 +86,7 < at >< at >
+ inline void copy(const T *pixel[3],
+ const unsigned long offset)
+ {
+- if (Init(pixel))
++ if (this->Init(pixel))
+ {
+ for (int j = 0; j < 3; j++)
+ OFBitmanipTemplate<T>::copyMem(pixel[j] + offset, this->Data[j], this->getCount());
+< at >< at > -102,6 +102,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dicocpt.h,v $
++ * Revision 1.13 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.12 2010-10-14 13:16:29 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicoflt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicoflt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicoflt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1998-2010, OFFIS e.V.
++ * Copyright (C) 1998-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomColorFlipTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:29 $
+- * CVS/RCS Revision: $Revision: 1.15 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.16 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -98,14 +98,14 < at >< at >
+ const int horz,
+ const int vert)
+ {
+- if (Init(pixel))
++ if (this->Init(pixel))
+ {
+ if (horz && vert)
+- flipHorzVert(pixel, this->Data);
++ this->flipHorzVert(pixel, this->Data);
+ else if (horz)
+- flipHorz(pixel, this->Data);
++ this->flipHorz(pixel, this->Data);
+ else if (vert)
+- flipVert(pixel, this->Data);
++ this->flipVert(pixel, this->Data);
+ }
+ }
+ };
+< at >< at > -118,6 +118,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dicoflt.h,v $
++ * Revision 1.16 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.15 2010-10-14 13:16:29 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicorot.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicorot.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicorot.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1998-2010, OFFIS e.V.
++ * Copyright (C) 1998-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomColorRotateTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:29 $
+- * CVS/RCS Revision: $Revision: 1.15 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.16 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -98,14 +98,14 < at >< at >
+ inline void rotate(const T *pixel[3],
+ const int degree)
+ {
+- if (Init(pixel))
++ if (this->Init(pixel))
+ {
+ if (degree == 90)
+- rotateRight(pixel, this->Data);
++ this->rotateRight(pixel, this->Data);
+ else if (degree == 180)
+- rotateTopDown(pixel, this->Data);
++ this->rotateTopDown(pixel, this->Data);
+ else if (degree == 270)
+- rotateLeft(pixel, this->Data);
++ this->rotateLeft(pixel, this->Data);
+ }
+ }
+ };
+< at >< at > -118,6 +118,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dicorot.h,v $
++ * Revision 1.16 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.15 2010-10-14 13:16:29 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicosct.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dicosct.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dicosct.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomColorScaleTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:29 $
+- * CVS/RCS Revision: $Revision: 1.21 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.22 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -107,8 +107,8 < at >< at >
+ inline void scale(const T *pixel[3],
+ const int interpolate)
+ {
+- if (Init(pixel))
+- scaleData(pixel, this->Data, interpolate);
++ if (this->Init(pixel))
++ this->scaleData(pixel, this->Data, interpolate);
+ }
+ };
+
+< at >< at > -120,6 +120,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dicosct.h,v $
++ * Revision 1.22 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.21 2010-10-14 13:16:29 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dihsvpxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dihsvpxt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dihsvpxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomHSVPixelTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:29 $
+- * CVS/RCS Revision: $Revision: 1.25 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.26 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -87,7 +87,7 < at >< at >
+ const unsigned long planeSize,
+ const int bits)
+ {
+- if (Init(pixel))
++ if (this->Init(pixel))
+ {
+ register T2 *r = this->Data[0];
+ register T2 *g = this->Data[1];
+< at >< at > -221,6 +221,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dihsvpxt.h,v $
++ * Revision 1.26 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.25 2010-10-14 13:16:29 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dipalpxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dipalpxt.h2010-10-14 13:16:29.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dipalpxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomPalettePixelTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:29 $
+- * CVS/RCS Revision: $Revision: 1.24 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.25 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -92,7 +92,7 < at >< at >
+ void convert(const T1 *pixel,
+ DiLookupTable *palette[3])
+ { // can be optimized if necessary !
+- if (Init(pixel))
++ if (this->Init(pixel))
+ {
+ register const T1 *p = pixel;
+ register T2 value = 0;
+< at >< at > -126,6 +126,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dipalpxt.h,v $
++ * Revision 1.25 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.24 2010-10-14 13:16:29 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dirgbpxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/dirgbpxt.h2010-10-14 13:16:30.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/dirgbpxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomRGBPixelTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:30 $
+- * CVS/RCS Revision: $Revision: 1.18 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.19 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -87,7 +87,7 < at >< at >
+ const unsigned long planeSize,
+ const int bits)
+ {
+- if (Init(pixel))
++ if (this->Init(pixel))
+ {
+ // use the number of input pixels derived from the length of the 'PixelData'
+ // attribute), but not more than the size of the intermediate buffer
+< at >< at > -129,9 +129,9 < at >< at >
+ {
+ register int j;
+ register unsigned long i;
+- for (i = 0; i < count; ++i) /* for all pixel ... */
++ for (i = 0; i < count; ++i) /* for all pixel ... */
+ for (j = 0; j < 3; ++j)
+- this->Data[j][i] = removeSign(*(p++), offset); /* ... copy planes */
++ this->Data[j][i] = removeSign(*(p++), offset); /* ... copy planes */
+ }
+ }
+ }
+< at >< at > -145,6 +145,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dirgbpxt.h,v $
++ * Revision 1.19 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.18 2010-10-14 13:16:30 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diybrpxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diybrpxt.h2010-10-14 13:16:30.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diybrpxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1998-2010, OFFIS e.V.
++ * Copyright (C) 1998-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomYBRPixelTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:30 $
+- * CVS/RCS Revision: $Revision: 1.19 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.20 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -91,7 +91,7 < at >< at >
+ const int bits,
+ const OFBool rgb)
+ {
+- if (Init(pixel))
++ if (this->Init(pixel))
+ {
+ const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1));
+ // use the number of input pixels derived from the length of the 'PixelData'
+< at >< at > -266,9 +266,9 < at >< at >
+ {
+ register int j;
+ register unsigned long i;
+- for (i = 0; i < count; ++i) /* for all pixel ... */
++ for (i = 0; i < count; ++i) /* for all pixel ... */
+ for (j = 0; j < 3; ++j)
+- this->Data[j][i] = removeSign(*(p++), offset); /* ... copy planes */
++ this->Data[j][i] = removeSign(*(p++), offset); /* ... copy planes */
+ }
+ }
+ }
+< at >< at > -295,6 +295,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: diybrpxt.h,v $
++ * Revision 1.20 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.19 2010-10-14 13:16:30 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyf2pxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diyf2pxt.h2010-10-14 13:16:30.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyf2pxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1998-2010, OFFIS e.V.
++ * Copyright (C) 1998-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomYBR422PixelTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:30 $
+- * CVS/RCS Revision: $Revision: 1.25 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.26 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -95,7 +95,7 < at >< at >
+ const int bits,
+ const OFBool rgb)
+ {
+- if (Init(pixel))
++ if (this->Init(pixel))
+ {
+ const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1));
+ register unsigned long i;
+< at >< at > -167,6 +167,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: diyf2pxt.h,v $
++ * Revision 1.26 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.25 2010-10-14 13:16:30 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyp2pxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimage/include/dcmtk/dcmimage/diyp2pxt.h2010-10-14 13:16:30.000000000 +0000
++++ dcmtk-3.6.0/dcmimage/include/dcmtk/dcmimage/diyp2pxt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1998-2010, OFFIS e.V.
++ * Copyright (C) 1998-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomYBRPart422PixelTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:30 $
+- * CVS/RCS Revision: $Revision: 1.23 $
++ * Update Date: $Date: 2011-11-17 16:13:14 $
++ * CVS/RCS Revision: $Revision: 1.24 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -91,7 +91,7 < at >< at >
+ void convert(const T1 *pixel,
+ const int bits)
+ {
+- if (Init(pixel))
++ if (this->Init(pixel))
+ {
+ register T2 *r = this->Data[0];
+ register T2 *g = this->Data[1];
+< at >< at > -147,6 +147,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: diyp2pxt.h,v $
++ * Revision 1.24 2011-11-17 16:13:14 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.23 2010-10-14 13:16:30 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/diflipt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/diflipt.h2010-10-14 13:16:26.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/diflipt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomFlipTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:26 $
+- * CVS/RCS Revision: $Revision: 1.23 $
++ * Update Date: $Date: 2011-11-17 16:13:16 $
++ * CVS/RCS Revision: $Revision: 1.24 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -129,7 +129,7 < at >< at >
+ else if (vert)
+ flipVert(src, dest);
+ else
+- copyPixel(src, dest);
++ this->copyPixel(src, dest);
+ }
+ }
+
+< at >< at > -345,6 +345,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: diflipt.h,v $
++ * Revision 1.24 2011-11-17 16:13:16 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.23 2010-10-14 13:16:26 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoflt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimoflt.h2010-10-14 13:16:26.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoflt.h2012-05-25 09:16:23.795876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomMonochromeFlipTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:26 $
+- * CVS/RCS Revision: $Revision: 1.15 $
++ * Update Date: $Date: 2011-11-17 16:13:16 $
++ * CVS/RCS Revision: $Revision: 1.16 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -106,11 +106,11 < at >< at >
+ if (this->Data != NULL)
+ {
+ if (horz && vert)
+- flipHorzVert(&pixel, &this->Data);
++ this->flipHorzVert(&pixel, &this->Data);
+ else if (horz)
+- flipHorz(&pixel, &this->Data);
++ this->flipHorz(&pixel, &this->Data);
+ else if (vert)
+- flipVert(&pixel, &this->Data);
++ this->flipVert(&pixel, &this->Data);
+ }
+ }
+ }
+< at >< at > -124,6 +124,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dimoflt.h,v $
++ * Revision 1.16 2011-11-17 16:13:16 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.15 2010-10-14 13:16:26 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h2010-10-14 13:16:26.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomMonochromeInputPixelTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:26 $
+- * CVS/RCS Revision: $Revision: 1.40 $
++ * Update Date: $Date: 2011-11-17 16:13:16 $
++ * CVS/RCS Revision: $Revision: 1.41 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -76,10 +76,10 < at >< at >
+ else if ((this->Modality != NULL) && this->Modality->hasRescaling())
+ {
+ rescale(pixel, this->Modality->getRescaleSlope(), this->Modality->getRescaleIntercept());
+- determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
++ this->determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
+ } else {
+ rescale(pixel); // "copy" or reference pixel data
+- determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
++ this->determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue()));
+ }
+ }
+ }
+< at >< at > -280,6 +280,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dimoipxt.h,v $
++ * Revision 1.41 2011-11-17 16:13:16 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.40 2010-10-14 13:16:26 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimorot.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimorot.h2010-10-14 13:16:26.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimorot.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomMonochromeRotateTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:26 $
+- * CVS/RCS Revision: $Revision: 1.16 $
++ * Update Date: $Date: 2011-11-17 16:13:16 $
++ * CVS/RCS Revision: $Revision: 1.17 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -105,11 +105,11 < at >< at >
+ if (this->Data != NULL)
+ {
+ if (degree == 90)
+- rotateRight(&pixel, &(this->Data));
++ this->rotateRight(&pixel, &(this->Data));
+ else if (degree == 180)
+- rotateTopDown(&pixel, &(this->Data));
++ this->rotateTopDown(&pixel, &(this->Data));
+ else if (degree == 270)
+- rotateLeft(&pixel, &(this->Data));
++ this->rotateLeft(&pixel, &(this->Data));
+ }
+ }
+ }
+< at >< at > -123,6 +123,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dimorot.h,v $
++ * Revision 1.17 2011-11-17 16:13:16 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.16 2010-10-14 13:16:26 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimosct.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dimosct.h2010-10-14 13:16:26.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dimosct.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomMonochromeScaleTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:26 $
+- * CVS/RCS Revision: $Revision: 1.20 $
++ * Update Date: $Date: 2011-11-17 16:13:16 $
++ * CVS/RCS Revision: $Revision: 1.21 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -124,7 +124,7 < at >< at >
+ {
+ const T value = OFstatic_cast(T, OFstatic_cast(double, DicomImageClass::maxval(bits)) *
+ OFstatic_cast(double, pvalue) / OFstatic_cast(double, DicomImageClass::maxval(WIDTH_OF_PVALUES)));
+- scaleData(&pixel, &this->Data, interpolate, value);
++ this->scaleData(&pixel, &this->Data, interpolate, value);
+ }
+ }
+ }
+< at >< at > -138,6 +138,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dimosct.h,v $
++ * Revision 1.21 2011-11-17 16:13:16 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.20 2010-10-14 13:16:26 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dirotat.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/dirotat.h2010-10-14 13:16:27.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/dirotat.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomRotateTemplate (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:27 $
+- * CVS/RCS Revision: $Revision: 1.21 $
++ * Update Date: $Date: 2011-11-17 16:13:16 $
++ * CVS/RCS Revision: $Revision: 1.22 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -132,7 +132,7 < at >< at >
+ else if (degree == 270)
+ rotateLeft(src, dest);
+ else
+- copyPixel(src, dest);
++ this->copyPixel(src, dest);
+ }
+
+
+< at >< at > -358,6 +358,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: dirotat.h,v $
++ * Revision 1.22 2011-11-17 16:13:16 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.21 2010-10-14 13:16:27 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/discalet.h
+===================================================================
+--- dcmtk-3.6.0.orig/dcmimgle/include/dcmtk/dcmimgle/discalet.h2010-10-14 13:16:27.000000000 +0000
++++ dcmtk-3.6.0/dcmimgle/include/dcmtk/dcmimgle/discalet.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 1996-2010, OFFIS e.V.
++ * Copyright (C) 1996-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -18,8 +18,8 < at >< at >
+ * Purpose: DicomScaleTemplates (Header)
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:16:27 $
+- * CVS/RCS Revision: $Revision: 1.35 $
++ * Update Date: $Date: 2011-11-17 16:13:16 $
++ * CVS/RCS Revision: $Revision: 1.36 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -206,12 +206,12 < at >< at >
+ (Left >= OFstatic_cast(signed long, Columns)) || (Top >= OFstatic_cast(signed long, Rows)))
+ { // no image to be displayed
+ DCMIMGLE_DEBUG("clipping area is fully outside the image boundaries");
+- fillPixel(dest, value); // ... fill bitmap
++ this->fillPixel(dest, value); // ... fill bitmap
+ }
+ else if ((this->Src_X == this->Dest_X) && (this->Src_Y == this->Dest_Y)) // no scaling
+ {
+ if ((Left == 0) && (Top == 0) && (Columns == this->Src_X) && (Rows == this->Src_Y))
+- copyPixel(src, dest); // copying
++ this->copyPixel(src, dest); // copying
+ else if ((Left >= 0) && (OFstatic_cast(Uint16, Left + this->Src_X) <= Columns) &&
+ (Top >= 0) && (OFstatic_cast(Uint16, Top + this->Src_Y) <= Rows))
+ clipPixel(src, dest); // clipping
+< at >< at > -567,7 +567,7 < at >< at >
+ if ((xtemp == NULL) || (xvalue == NULL))
+ {
+ DCMIMGLE_ERROR("can't allocate temporary buffers for interpolation scaling");
+- clearPixel(dest);
++ this->clearPixel(dest);
+ } else {
+ for (int j = 0; j < this->Planes; ++j)
+ {
+< at >< at > -905,7 +905,7 < at >< at >
+ if (pTemp == NULL)
+ {
+ DCMIMGLE_ERROR("can't allocate temporary buffer for interpolation scaling");
+- clearPixel(dest);
++ this->clearPixel(dest);
+ } else {
+
+ /*
+< at >< at > -1029,7 +1029,7 < at >< at >
+ if (pTemp == NULL)
+ {
+ DCMIMGLE_ERROR("can't allocate temporary buffer for interpolation scaling");
+- clearPixel(dest);
++ this->clearPixel(dest);
+ } else {
+
+ /*
+< at >< at > -1190,6 +1190,9 < at >< at >
+ *
+ * CVS/RCS Log:
+ * $Log: discalet.h,v $
++ * Revision 1.36 2011-11-17 16:13:16 joergr
++ * Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++ *
+ * Revision 1.35 2010-10-14 13:16:27 joergr
+ * Updated copyright header. Added reference to COPYRIGHT file.
+ *
+Index: dcmtk-3.6.0/ofstd/include/dcmtk/ofstd/ofoset.h
+===================================================================
+--- dcmtk-3.6.0.orig/ofstd/include/dcmtk/ofstd/ofoset.h2010-10-14 13:15:50.000000000 +0000
++++ dcmtk-3.6.0/ofstd/include/dcmtk/ofstd/ofoset.h2012-05-25 09:16:23.799876809 +0000
+< at >< at > -1,6 +1,6 < at >< at >
+ /*
+ *
+- * Copyright (C) 2002-2010, OFFIS e.V.
++ * Copyright (C) 2002-2011, OFFIS e.V.
+ * All rights reserved. See COPYRIGHT file for details.
+ *
+ * This software and supporting documentation were developed by
+< at >< at > -19,8 +19,8 < at >< at >
+ * of an arbitrary type.
+ *
+ * Last Update: $Author: joergr $
+- * Update Date: $Date: 2010-10-14 13:15:50 $
+- * CVS/RCS Revision: $Revision: 1.11 $
++ * Update Date: $Date: 2011-11-17 16:13:18 $
++ * CVS/RCS Revision: $Revision: 1.12 $
+ * Status: $State: Exp $
+ *
+ * CVS/RCS Log at end of file
+< at >< at > -146,7 +146,7 < at >< at >
+ {
+ // if size equals num, we need more space
+ if( this->size == this->num )
+- Resize( this->size * 2 );
++ this->Resize( this->size * 2 );
+
+ // copy item
+ T *newItem = new T( item );
+< at >< at > -189,7 +189,7 < at >< at >
+ {
+ // if size equals num, we need more space
+ if( this->size == this->num )
+- Resize( this->size * 2 );
++ this->Resize( this->size * 2 );
+
+ // copy item
+ T *newItem = new T( item );
+< at >< at > -508,6 +508,9 < at >< at >
+ /*
+ ** CVS/RCS Log:
+ ** $Log: ofoset.h,v $
++** Revision 1.12 2011-11-17 16:13:18 joergr
++** Minor fixes to keep XCode 4.2 on Mac OS X Lion (clang compiler) quiet.
++**
+ ** Revision 1.11 2010-10-14 13:15:50 joergr
+ ** Updated copyright header. Added reference to COPYRIGHT file.
+ **
Modified: trunk/packages/dcmtk/trunk/debian/patches/series
===================================================================
--- trunk/packages/dcmtk/trunk/debian/patches/series2012-05-25 08:46:12 UTC (rev 10999)
+++ trunk/packages/dcmtk/trunk/debian/patches/series2012-05-25 09:51:25 UTC (rev 11000)
< at >< at > -9,3 +9,4 < at >< at >
dcmtk_version_number.patch
regression_stacksequenceisodd.patch
removecharls.patch
+bug674361.patch
Modified: trunk/packages/dcmtk/trunk/debian/rules
===================================================================
--- trunk/packages/dcmtk/trunk/debian/rules2012-05-25 08:46:12 UTC (rev 10999)
+++ trunk/packages/dcmtk/trunk/debian/rules2012-05-25 09:51:25 UTC (rev 11000)
< at >< at > -1,10 +1,4 < at >< at >
#!/usr/bin/make -f
-# debian/rules for dcmtk
-# Authors: Juergen Salk <juergen.salk< at >gmx.de>
-# Mathieu Malaterre <mathieu.malaterre< at >gmail.com>
-
-include /usr/share/quilt/quilt.make
-
#export DH_VERBOSE=1
# These are used for cross-compiling and for saving the configure script
< at >< at > -26,15 +20,11 < at >< at >
# Library version
LIB_VERSION=2.0.0
-CFLAGS = -Wall -g
-LDFLAGS = -Wl,--no-as-needed
+export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/buildflags.mk
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
-CFLAGS += -O0
-else
-CFLAGS += -O2
-endif
-
config/config.status: configure
dh_testdir
< at >< at > -69,7 +59,7 < at >< at >
--with-openssl
-build-arch: $(QUILT_STAMPFN) config/config.status build-arch-stamp
+build-arch: config/config.status build-arch-stamp
build-arch-stamp:
dh_testdir
< at >< at > -89,7 +79,7 < at >< at >
# utilities dynamically against the shared library versions.
mv config/Makefile.def config/Makefile.def.static && \
-sed -e '/^CFLAGS =/s/-O/-fPIC $(CFLAGS)/' -e '/^CXXFLAGS =/s/-O/-fPIC $(CXXFLAGS)/' \
+sed -e '/^CFLAGS =/s/-O/-fPIC/' -e '/^CXXFLAGS =/s/-O/-fPIC/' \
-e '/^AR =/s/ar/gcc/' -e '/^ARFLAGS =/s/cruv/-shared -Wl,-soname,\$$\< at >.2 -o/' \
-e '/^LIBEXT =/s/a/so/' -e '/^RANLIB =/s/ranlib/:/' \
<config/Makefile.def.static >config/Makefile.def && \
< at >< at > -111,7 +101,7 < at >< at >
build: build-arch
-clean: unpatch
+clean:
dh_testdir
dh_testroot
if [ -d config/backup ] ; then cd config; mv backup/* . ; rm -rf backup ; fi
</pre>
Mathieu Malaterre
2012-05-25T09:51:26
-
r10999 - trunk/packages/sift/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11372
<pre>Author: tille
Date: 2012-05-25 08:46:12 +0000 (Fri, 25 May 2012)
New Revision: 10999
Added:
trunk/packages/sift/trunk/debian/upstream
Modified:
trunk/packages/sift/trunk/debian/changelog
Log:
Citation of the day
Modified: trunk/packages/sift/trunk/debian/changelog
===================================================================
--- trunk/packages/sift/trunk/debian/changelog2012-05-24 21:26:20 UTC (rev 10998)
+++ trunk/packages/sift/trunk/debian/changelog2012-05-25 08:46:12 UTC (rev 10999)
< at >< at > -1,3 +1,9 < at >< at >
+sift (4.0.3b-4) UNRELEASED; urgency=low
+
+ * debian/upstream: Add citations
+
+ -- Andreas Tille <tille< at >debian.org> Fri, 25 May 2012 10:45:33 +0200
+
sift (4.0.3b-3) unstable; urgency=low
* Added patches from Michael Bienia <geser< at >ubuntu.com>.
Added: trunk/packages/sift/trunk/debian/upstream
===================================================================
--- trunk/packages/sift/trunk/debian/upstream (rev 0)
+++ trunk/packages/sift/trunk/debian/upstream2012-05-25 08:46:12 UTC (rev 10999)
< at >< at > -0,0 +1,55 < at >< at >
+Reference:
+ - Author: Prateek Kumar and Steven Henikoff and Pauline C Ng
+ Title: Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
+ Journal: Nature Protocols
+ Year: 2009
+ Volume: 4
+ Number: 7
+ Pages: 1073-81
+ DOI: 10.1038/nprot.2009.86
+ PMID: 19561590
+ URL: http://www.nature.com/nprot/journal/v4/n7/full/nprot.2009.86.html
+ eprint: http://www.nature.com/nprot/journal/v4/n7/pdf/nprot.2009.86.pdf
+ - Author: Pauline C Ng and Steven Henikoff
+ Title: Predicting the effects of amino acid substitutions on protein function
+ Journal: Annu Rev Genomics Hum Genet.
+ Year: 2006
+ Volume: 7
+ Pages: 61-80
+ DOI: 10.1146/annurev.genom.7.080505.115630
+ PMID: 16824020
+ URL: http://www.annualreviews.org/doi/abs/10.1146/annurev.genom.7.080505.115630
+ eprint: http://www.annualreviews.org/doi/pdf/10.1146/annurev.genom.7.080505.115630
+ - Author: Pauline C Ng and Steven Henikoff
+ Title: "SIFT: Predicting amino acid changes that affect protein function"
+ Journal: Nucleic Acids Research
+ Year: 2003
+ Volume: 31
+ Number: 13
+ Pages: 3812-4
+ DOI: 10.1093/nar/gkg509
+ PMID: 12824425
+ URL: http://nar.oxfordjournals.org/content/31/13/3812.abstract
+ eprint: http://nar.oxfordjournals.org/content/31/13/3812.full.pdf+html
+ - Author: Pauline C Ng and Steven Henikoff
+ Title: "Accounting for human polymorphisms predicted to affect protein function"
+ Journal: Genome Research
+ Year: 2002
+ Volume: 12
+ Number: 3
+ Pages: 436-46
+ DOI: 10.1101/gr.212802
+ PMID: 11875032
+ URL: http://genome.cshlp.org/content/12/3/436
+ eprint: http://genome.cshlp.org/content/12/3/436.full.pdf+html
+ - Author: Pauline C Ng and Steven Henikoff
+ Title: Predicting deleterious amino acid substitutions
+ Journal: Genome Research
+ Year: 2001
+ Volume: 11
+ Number: 5
+ Pages: 863-74
+ DOI: 10.1101/gr.176601
+ PMID: 11337480
+ URL: http://genome.cshlp.org/content/11/5/863
+ eprint: http://genome.cshlp.org/content/11/5/863.full.pdf+html
</pre>
Andreas Tille
2012-05-25T08:46:13
-
r10998 - in trunk/packages: . amos amos/trunkamos/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11371
<pre>Author: tille
Date: 2012-05-24 21:26:20 +0000 (Thu, 24 May 2012)
New Revision: 10998
Added:
trunk/packages/amos/
trunk/packages/amos/trunk/
trunk/packages/amos/trunk/debian/
trunk/packages/amos/trunk/debian/changelog
trunk/packages/amos/trunk/debian/compat
trunk/packages/amos/trunk/debian/control
trunk/packages/amos/trunk/debian/copyright
trunk/packages/amos/trunk/debian/upstream
trunk/packages/amos/trunk/debian/watch
Log:
Add machine-readable data for amos-assembler and hawkeye which both build from the same source
Added: trunk/packages/amos/trunk/debian/changelog
===================================================================
--- trunk/packages/amos/trunk/debian/changelog (rev 0)
+++ trunk/packages/amos/trunk/debian/changelog2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1,5 < at >< at >
+amos (3.1.0-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Andreas Tille <tille< at >debian.org> Thu, 24 May 2012 14:30:13 +0200
Added: trunk/packages/amos/trunk/debian/compat
===================================================================
--- trunk/packages/amos/trunk/debian/compat (rev 0)
+++ trunk/packages/amos/trunk/debian/compat2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1 < at >< at >
+9
Added: trunk/packages/amos/trunk/debian/control
===================================================================
--- trunk/packages/amos/trunk/debian/control (rev 0)
+++ trunk/packages/amos/trunk/debian/control2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1,55 < at >< at >
+Source: amos
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille< at >debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.3
+Homepage: http://amos.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/amos/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/amos/trunk/
+
+Package: amos-assembler
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: modular whole genome assembler
+ The AMOS consortium is committed to the development of open-source
+ whole genome assembly software. The project acronym (AMOS) represents
+ our primary goal - to produce A Modular, Open-Source whole genome
+ assembler. Open-source so that everyone is welcome to contribute and
+ help build outstanding assembly tools, and modular in nature so that
+ new contributions can be easily inserted into an existing assembly
+ pipeline. This modular design will foster the development of new
+ assembly algorithms and allow the AMOS project to continually grow
+ and improve in hopes of eventually becoming a widely accepted and
+ deployed assembly infrastructure. In this sense, AMOS is both a
+ design philosophy and a software system.
+
+Package: hawkeye
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Interactive Visual Analytics Tool for Genome Assemblies
+ Genome assembly remains an inexact science. Even when accomplished
+ with the best software available, the assembly of a genome often
+ contains numerous errors, both small and large. Hawkeye is a visual
+ analytics tool for genome assembly analysis and validation, designed
+ to aid in identifying and correcting assembly errors. Hawkeye blends
+ the best practices from information and scientific visualization to
+ facilitate inspection of large-scale assembly data while minimizing
+ the time needed to detect mis-assemblies and make accurate judgments
+ of assembly quality.
+ .
+ All levels of the assembly data hierarchy are made accessible to
+ users, along with summary statistics and common assembly metrics. A
+ ranking component guides investigation towards likely mis-assemblies
+ or interesting features to support the task at hand. Wherever
+ possible, high-level overviews, dynamic filtering, and automated
+ clustering are leveraged to focus attention and highlight anomalies
+ in the data. Hawkeyes effectiveness has been proven on several genome
+ projects, where it has been used both to improve quality and to
+ validate the correctness of complex genomes.
+ .
+ Hawkeye is compatible with most widely used assemblers, including
+ Phrap, ARACHNE, Celera Assembler, Newbler, AMOS, and assemblies
+ deposited in the NCBI Assembly Archive.
Added: trunk/packages/amos/trunk/debian/copyright
===================================================================
--- trunk/packages/amos/trunk/debian/copyright (rev 0)
+++ trunk/packages/amos/trunk/debian/copyright2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1,11 < at >< at >
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: AMOS
+Source: http://sourceforge.net/projects/amos/files/amos/
+
+Files: *
+Copyright: © 2002-2011 AMOS consortium
+License: Artistic
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille< at >debian.org>
+License: Artistic
Added: trunk/packages/amos/trunk/debian/upstream
===================================================================
--- trunk/packages/amos/trunk/debian/upstream (rev 0)
+++ trunk/packages/amos/trunk/debian/upstream2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1,32 < at >< at >
+Reference:
+ - Author: Michael C. Schatz and Adam M. Phillippy and Daniel D. Sommer and Arthur L. Delcher and Daniela Puiu and Giuseppe Narzisi and Steven L. Salzberg and Mihai Pop
+ Title: "Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies"
+ Journal: Briefings in Bioinform
+ Year: 2011
+ DOI: 10.1093/bib/bbr074
+ PMID: 22199379
+ URL: http://bib.oxfordjournals.org/content/early/2011/12/23/bib.bbr074
+ eprint: http://bib.oxfordjournals.org/content/early/2011/12/23/bib.bbr074.full.pdf+html
+ - Debian-Package: hawkeye
+ Author: Michael C Schatz and Adam M Phillippy and Ben Shneiderman and Steven L Salzberg
+ Title: "Hawkeye: an interactive visual analytics tool for genome assemblies"
+ Journal: Genome Biology
+ Year: 2007
+ Volume: 8
+ Number: 3
+ Pages: R34
+ DOI: 10.1186/gb-2007-8-3-r34
+ PMID: 17349036
+ URL: http://genomebiology.com/2007/8/3/R34
+ eprint: http://genomebiology.com/content/pdf/gb-2007-8-3-r34.pdf
+ - Debian-Package: amos-assembler
+ Author: Todd J Treangen and Dan D Sommer and Florent E Angly and Sergey Koren and Mihai Pop
+ Title: Next generation sequence assembly with AMOS
+ Journal: Curr Protoc Bioinformatics.
+ Year: 2011
+ Volume: Chapter 11
+ Pages: Unit 11.8
+ DOI: 10.1002/0471250953.bi1108s33
+ PMID: 21400694
+ URL: http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1108s33/abstract
+ eprint: http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1108s33/pdf
Added: trunk/packages/amos/trunk/debian/watch
===================================================================
--- trunk/packages/amos/trunk/debian/watch (rev 0)
+++ trunk/packages/amos/trunk/debian/watch2012-05-24 21:26:20 UTC (rev 10998)
< at >< at > -0,0 +1,2 < at >< at >
+version=3
+http://sf.net/amos/amos-([.\d]+)\.tar\.gz
_______________________________________________
debian-med-commit mailing list
debian-med-commit< at >lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit</pre>
Andreas Tille
2012-05-24T21:26:20
-
r10997 - trunk/packages/pdb2pqr/trunk/debian
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11370
<pre>Author: mbanck
Date: 2012-05-24 15:30:49 +0000 (Thu, 24 May 2012)
New Revision: 10997
Modified:
trunk/packages/pdb2pqr/trunk/debian/upstream
Log:
Add name, homepage and registration fields to upstream metadata
Modified: trunk/packages/pdb2pqr/trunk/debian/upstream
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/upstream2012-05-24 15:23:06 UTC (rev 10996)
+++ trunk/packages/pdb2pqr/trunk/debian/upstream2012-05-24 15:30:49 UTC (rev 10997)
< at >< at > -1,3 +1,6 < at >< at >
+Name: PDB2PQR
+Homepage: http://www.poissonboltzmann.org/pdb2pqr
+Registration: http://spreadsheets.google.com/viewform?hl=en&formkey=dHFpa3Nvcnl0cjR1U3g3UTdSYU1pWWc6MA..
Reference:
- Author: Todd J Dolinsky and Paul Czodrowski and Hui Li and Jens E Nielsen and Jan H Jensen and Gerhard Klebe and Nathan A Baker
Title: "PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations"
</pre>
Michael Banck
2012-05-24T15:30:50
-
r10996 - in trunk/packages/libforester-java/trunk: .debian debian/binary debian/patches debian/source
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11369
<pre>Author: osallou
Date: 2012-05-24 15:23:06 +0000 (Thu, 24 May 2012)
New Revision: 10996
Added:
trunk/packages/libforester-java/trunk/debian/
trunk/packages/libforester-java/trunk/debian/binary/
trunk/packages/libforester-java/trunk/debian/binary/forester
trunk/packages/libforester-java/trunk/debian/changelog
trunk/packages/libforester-java/trunk/debian/compat
trunk/packages/libforester-java/trunk/debian/control
trunk/packages/libforester-java/trunk/debian/copyright
trunk/packages/libforester-java/trunk/debian/docs
trunk/packages/libforester-java/trunk/debian/forester.install
trunk/packages/libforester-java/trunk/debian/get-orig-source.sh
trunk/packages/libforester-java/trunk/debian/libforester-java-doc.doc-base
trunk/packages/libforester-java/trunk/debian/libforester-java-doc.install
trunk/packages/libforester-java/trunk/debian/libforester-java.jlibs
trunk/packages/libforester-java/trunk/debian/patches/
trunk/packages/libforester-java/trunk/debian/patches/change_itext_packagename.patch
trunk/packages/libforester-java/trunk/debian/patches/fix_jar_path.patch
trunk/packages/libforester-java/trunk/debian/patches/series
trunk/packages/libforester-java/trunk/debian/rules
trunk/packages/libforester-java/trunk/debian/source/
trunk/packages/libforester-java/trunk/debian/source/format
Log:
[svn-inject] Applying Debian modifications (0.971-1) to trunk
Property changes on: trunk/packages/libforester-java/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/libforester-java/trunk/debian/binary/forester
===================================================================
--- trunk/packages/libforester-java/trunk/debian/binary/forester (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/binary/forester2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,3 < at >< at >
+#!/bin/bash
+
+java -jar /usr/share/java/forester.jar
Property changes on: trunk/packages/libforester-java/trunk/debian/binary/forester
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/libforester-java/trunk/debian/changelog
===================================================================
--- trunk/packages/libforester-java/trunk/debian/changelog (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/changelog2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,7 < at >< at >
+libforester-java (0.971-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #674269)
+ * Wait to know which revision in SVN we should take
+ * Ask upstream to put jars with version
+
+ -- Olivier Sallou <osallou< at >debian.org> Thu, 24 May 2012 12:28:55 +0200
Added: trunk/packages/libforester-java/trunk/debian/compat
===================================================================
--- trunk/packages/libforester-java/trunk/debian/compat (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/compat2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1 < at >< at >
+8
Added: trunk/packages/libforester-java/trunk/debian/control
===================================================================
--- trunk/packages/libforester-java/trunk/debian/control (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/control2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,39 < at >< at >
+Source: libforester-java
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging< at >lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Olivier Sallou <osallou< at >debian.org>
+Build-Depends: debhelper (>= 8.0.0),
+ default-jdk, junit4, javahelper (>=0.25), libcommons-codec, libitext-java
+Standards-Version: 3.9.3
+Homepage: http://code.google.com/p/forester
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/forester/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/forester/trunk/
+
+Package: forester
+Architecture: all
+Depends: ${misc:Depends}, libforester-java
+Description: Graphical vizualiation tool Archaeopteryx
+ Archaeopteryx is a software tool for the visualization, analysis,
+ and editing of potentially large and highly annotated phylogenetic trees.
+ It can be used both as applet (ArchaeopteryxA and ArchaeopteryxE) and
+ as a standalone application.
+
+Package: libforester-java
+Architecture: all
+Depends: ${misc:Depends},
+ libcommons-codec, libitext-java
+Description: Libraries for evolutionary biology and comparative genomics research
+ Forester is a library of Java software for phylogenomics
+ and evolutionary biology research. It can be used to read or
+ write phylogenetic trees, export trees to graphics file,...
+
+Package: libforester-java-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Description: [Biology] Documentation for forester
+ Forester is a library of Java software for phylogenomics
+ and evolutionary biology research. This package contains the
+ JavaDoc documentation.
Added: trunk/packages/libforester-java/trunk/debian/copyright
===================================================================
--- trunk/packages/libforester-java/trunk/debian/copyright (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/copyright2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,44 < at >< at >
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: forester
+Source: http://code.google.com/p/forester
+
+Files: *
+Copyright: 2010 Christian M. Zmasek
+ 2010 Sanford-Burnham Medical Research Institute
+License: LGPL 2.1+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ .
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+Files: debian/*
+Copyright: 2012 Olivier Sallou <osallou< at >debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
Added: trunk/packages/libforester-java/trunk/debian/docs
===================================================================
Added: trunk/packages/libforester-java/trunk/debian/forester.install
===================================================================
--- trunk/packages/libforester-java/trunk/debian/forester.install (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/forester.install2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1 < at >< at >
+debian/binary/forester usr/bin
Added: trunk/packages/libforester-java/trunk/debian/get-orig-source.sh
===================================================================
--- trunk/packages/libforester-java/trunk/debian/get-orig-source.sh (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/get-orig-source.sh2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,17 < at >< at >
+#!/bin/bash
+
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`dpkg-parsechangelog | awk '/^Version/ { print $2 }' | cut -d "-" -f1`
+version=$VERSION.svn.`date +"%Y%m%d"|tr -d '\n'`
+targetdir=libforester-java-$version
+origtargz=libforester-java_$VERSION.orig.tar.gz
+cd ..
+mkdir $targetdir
+svn checkout http://forester.googlecode.com/svn/forester/java $targetdir/java
+svn checkout http://forester.googlecode.com/svn/forester/resources $targetdir/resources
+find $targetdir -name ".svn" | xargs -r rm -r
+find $targetdir -name "*.jar" | xargs -r rm -r
+tar czf $origtargz $targetdir
+rm -rf $targetdir
+
Property changes on: trunk/packages/libforester-java/trunk/debian/get-orig-source.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/libforester-java/trunk/debian/libforester-java-doc.doc-base
===================================================================
--- trunk/packages/libforester-java/trunk/debian/libforester-java-doc.doc-base (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/libforester-java-doc.doc-base2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,12 < at >< at >
+Document: forester
+Title: forester API
+Author: Forester developers
+Abstract: Javadoc-generated API for the forester library.
+ Forester is a library of Java software for phylogenomics
+ and evolutionary biology research. It can be used to read or
+ write phylogenetic trees, export trees to graphics file,...
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/libforester-java/api/index.html
+Files: /usr/share/doc/libforester-java/api/*.html /usr/share/doc/libforester-java/api/*/*/*/*.html /usr/share/doc/libforester-java/api/*/*/*/*/*.html /usr/share/doc/libforester-java/api/*/*/*/*/*/*.html
Added: trunk/packages/libforester-java/trunk/debian/libforester-java-doc.install
===================================================================
--- trunk/packages/libforester-java/trunk/debian/libforester-java-doc.install (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/libforester-java-doc.install2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1 < at >< at >
+doc/* /usr/share/doc/libforester-java/api/
Added: trunk/packages/libforester-java/trunk/debian/libforester-java.jlibs
===================================================================
--- trunk/packages/libforester-java/trunk/debian/libforester-java.jlibs (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/libforester-java.jlibs2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1 < at >< at >
+java/forester.jar
Added: trunk/packages/libforester-java/trunk/debian/patches/change_itext_packagename.patch
===================================================================
--- trunk/packages/libforester-java/trunk/debian/patches/change_itext_packagename.patch (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/patches/change_itext_packagename.patch2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,29 < at >< at >
+Author: Olivier Sallou <osallou< at >debian.org>
+Subject: change package name for itext
+Description: Upstream refers to com.itext hwile Debian package
+ itext use package name com.lowagie. Replace in the file the package
+ name references
+Last-Updated: 24/05/12
+--- a/java/src/org/forester/archaeopteryx/PdfExporter.java
++++ b/java/src/org/forester/archaeopteryx/PdfExporter.java
+< at >< at > -35,13 +35,13 < at >< at >
+
+ import org.forester.phylogeny.Phylogeny;
+
+-import com.itextpdf.text.Document;
+-import com.itextpdf.text.DocumentException;
+-import com.itextpdf.text.FontFactory;
+-import com.itextpdf.text.Rectangle;
+-import com.itextpdf.text.pdf.DefaultFontMapper;
+-import com.itextpdf.text.pdf.PdfContentByte;
+-import com.itextpdf.text.pdf.PdfWriter;
++import com.lowagie.text.Document;
++import com.lowagie.text.DocumentException;
++import com.lowagie.text.FontFactory;
++import com.lowagie.text.Rectangle;
++import com.lowagie.text.pdf.DefaultFontMapper;
++import com.lowagie.text.pdf.PdfContentByte;
++import com.lowagie.text.pdf.PdfWriter;
+
+ /*
+ *
Added: trunk/packages/libforester-java/trunk/debian/patches/fix_jar_path.patch
===================================================================
--- trunk/packages/libforester-java/trunk/debian/patches/fix_jar_path.patch (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/patches/fix_jar_path.patch2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,68 < at >< at >
+Author: Olivier Sallou <osallou< at >debian.org>
+Subject: Change dependency libraries path
+Description: Use Debian libraries instead of upstream
+ included ones
+Last-Updated: 24/05/12
+--- a/java/build.xml
++++ b/java/build.xml
+< at >< at > -3,9 +3,9 < at >< at >
+
+ <property name="src.dir" value="src" />
+ <property name="classes.dir" value="classes" />
+-<property name="jars.dir" value="resources" />
+-<property name="itextjar" value="${jars.dir}/itextpdf-5.1.0.jar" />
+-<property name="commonscodecjar" value="${jars.dir}/commons-codec-1.5.jar" />
++<property name="jars.dir" value="/usr/share/java" />
++<property name="itextjar" value="${jars.dir}/itext.jar" />
++<property name="commonscodecjar" value="${jars.dir}/commons-codec.jar" />
+ <property name="forester_jar" value="forester.jar" />
+ <property name="archaeopteryx_applets_jar" value="archaeopteryx_applets.jar" />
+
+< at >< at > -40,34 +40,15 < at >< at >
+ </target>
+
+ <target name="jar" description="JARs the classes files" depends="compile,copy_resources">
+-<unjar src="${itextjar}" dest="${classes.dir}">
+- <patternset>
+- <include name="**/*.class" />
+- <include name="**/*.afm" />
+- <include name="**/*.txt" />
+- <exclude name="**/*Test*.class" />
+- </patternset>
+- </unjar>
+- <unjar src="${commonscodecjar}" dest="${classes.dir}">
+- <patternset>
+- <include name="**/*.class" />
+- <exclude name="**/*Test*.class" />
+- </patternset>
+- </unjar>
+ <jar level="9" destfile="${forester_jar}" basedir="${classes.dir}" excludes="**/Test.class" duplicate="fail" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="org.forester.archaeopteryx.Archaeopteryx" />
++<attribute name="Class-Path" value="${itextjar};${commonscodecjar}"/>
+ </manifest>
+ </jar>
+ </target>
+
+ <target name="jar_applets_only" description="JARs the classes files" depends="compile_applets_only,copy_resources">
+-<unjar src="${commonscodecjar}" dest="${classes.dir}">
+- <patternset>
+- <include name="**/*.class" />
+- <exclude name="**/*Test*.class" />
+- </patternset>
+- </unjar>
+ <jar level="9" destfile="${archaeopteryx_applets_jar}" basedir="${classes.dir}" excludes="org/forester/application/**
+ org/forester/development/**
+ org/forester/evoinference/**
+< at >< at > -87,4 +68,11 < at >< at >
+ <target name="applets_only" description="" depends="jar_applets_only">
+ </target>
+
++ <target name="javadoc">
++ <mkdir dir="../doc"/>
++ <javadoc destdir="../doc" sourcepath="${src.dir}" >
++ <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
++ </javadoc>
++ </target>
++
+ </project>
Added: trunk/packages/libforester-java/trunk/debian/patches/series
===================================================================
--- trunk/packages/libforester-java/trunk/debian/patches/series (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/patches/series2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,2 < at >< at >
+fix_jar_path.patch
+change_itext_packagename.patch
Added: trunk/packages/libforester-java/trunk/debian/rules
===================================================================
--- trunk/packages/libforester-java/trunk/debian/rules (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/rules2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1,19 < at >< at >
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+dh $< at > --with javahelper
+
+override_dh_auto_build:
+cd java && ant
+cd java && ant javadoc
+
+override_dh_clean:
+cd java && ant clean
+rm -rf doc
+dh_clean
+
+get-orig-source:
+debian/get-orig-source.sh
Property changes on: trunk/packages/libforester-java/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/libforester-java/trunk/debian/source/format
===================================================================
--- trunk/packages/libforester-java/trunk/debian/source/format (rev 0)
+++ trunk/packages/libforester-java/trunk/debian/source/format2012-05-24 15:23:06 UTC (rev 10996)
< at >< at > -0,0 +1 < at >< at >
+3.0 (quilt)
</pre>
Olivier Sallou
2012-05-24T15:23:06
-
r10995 - trunk/packages/libforester-java
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11368
<pre>Author: osallou
Date: 2012-05-24 15:23:01 +0000 (Thu, 24 May 2012)
New Revision: 10995
Added:
trunk/packages/libforester-java/trunk/
Log:
Creating trunk directory
</pre>
Olivier Sallou
2012-05-24T15:23:02
-
r10994 - in trunk/packages: . libforester-java
http://comments.gmane.org/gmane.linux.debian.devel.medical.scm/11367
<pre>Author: osallou
Date: 2012-05-24 15:22:57 +0000 (Thu, 24 May 2012)
New Revision: 10994
Added:
trunk/packages/libforester-java/
trunk/packages/libforester-java/tags/
Log:
[svn-inject] Creating libforester-java/tags/ directory.
</pre>
Olivier Sallou
2012-05-24T15:22:57
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